Feature finding with MZmine2

Please follow this (link) to install the software and dependencies.

Complete workflow view

_images/Workflow_mzmine.pngcomplete workflow view

1. Start mzMine2

_images/1_Start.pngstart mzMine

2. Click on raw data import in drop down menu and select .mzxml files

_images/2_import-raw.pngimport data

3. Click on mass detection in drop down menu

_images/3_mass-detection.pngmass detection

4. Specify intensity cut-off and mass list

_images/4_mass-detection_select-cutoff_preview.pngspecify intensity cut-off

5. Build XICs with chromatogram builder

_images/5_Chrom-builder.pngBuild XICs with chromatogram builder

6. Specify mass list, mass tolerance min. time span and min. hight

_images/6_Chrom-builder_parameters.pngSpecify mass list, mass tolerance min. time span and min. hight

7. Deconvolute isobaric peaks with chromatogram deconvolution

_images/7_deconv.pngDeconvolute isobaric peaks with chromatogram deconvolution

8. Specify algorithm (base line cut-off or local minimum search and parmaters

_images/8_deconv_parameters.pngSpecify algorithm (base line cut-off or local minimum search and parmaters

9. Perform deisotopization through isotope peak grouper

_images/9_de-isotope.pngPerform deisotopization through isotope peak grouper

10. Specify parameters for isotope peak grouping

_images/10_de-isotope_parameters.pngSpecify parameters for isotope peak grouping

11. Align XICs from different sample to one matrix

_images/11_aligner.pngAlign XICs from different sample to one matrix

12. Specify join aligner parameters

_images/12_aligner_parameter.pngSpecify join aligner parameters

13. [optional] Filter aligned feature matrix with peak list row filter

_images/13_filter.pngFilter aligned feature matrix with peak list row filter

14. [optional] Depending of your experimental design use n minimum peaks in a row (n should be around the number of replicates or samples you expect to be similar) and 2-3 minimum peaks per isotope pattern

_images/14_filter_parameter.pnguse n minimum peaks in a row

15. [optional] You gap filling the re-analyses missed peaks and fill gaps in the feature matrix

_images/15_gap-filling.pngYou gap filling the re-analyses missed peaks and fill gaps in the feature matrix

16. [optional] Depending on experimental design you can normalize your peak intensities to internal standards, TICs or total peak area.

_images/16_gap-filling_parameters.pngnormalize your peak intensities to internal standards, TICs or total peak area

17. [optional] Specify normalization parameters

_images/17_norm.pngSpecify normalization parameters

18. Export your matrix as .csv file for down stream data analysis

_images/18_norm_parameters.pngExport your matrix as .csv file for down stream data analysis

19. select file name and parameters you want to export

_images/19_exp.pngselect file name and parameters you want to export

_images/20_exp_parmeters.pngselect file name and parameters you want to export

Here is also a video for MZmine 2 documentation:

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